Decline Inducing Citrus Tristeza Virus-Vt/kpg3 Genotype Occurs Predominantly in Citrus Orchards of Northeast India

Northeast (NE) India is known to produce different kinds of citrus species. Citrus tristeza virus (CTV), brown citrus aphid (Toxoptera citricidus) transmitted closterovirus, is a major problem to cause citrus decline in this region. CTV has destroyed more than one million of citrus trees in India. CTV contains flexuous filamentous particles (2000 × 11 nm) and positive sense ssRNA genome of about 19.3 kb having 12 ORFs encoding about 19 proteins. The survey was made in different citrus orchards of Assam to study the disease incidence and genetic diversity of CTV. Several citrus samples were collected from Citrus reticulata cvs Khasi, Kinnow and Nagpur mandarin; C. sinensis cvs Sweet orange and Valencia orange; C. limon cv. Assam lemon; C. jambhiri cv. Rough lemon, of three citrus Farms of Assam; HRS farm, AAU, Guwahati; CEC, Kamrup Rural; and URF, AAU, Jorhat. Different kinds of symptoms like decline, chlorosis, yellowing and poor growth with stunting of citrus trees were observed in these orchards. Based on Direct antigen coated-enzyme link immunosorbent assay (DAC-ELISA) and Polymerase chain reaction (PCR) it was found that incidence CTV ranged from 40.9 to 85.54% and the overall incidence of 65.7% was estimated. Twenty-one isolates of CTV, designated as CTV-Asm 1 to CTV-Asm 21 were collected from different locations and characterized based sequence analysis of 404 nt fragment of 5’ORF1a gene of CTV genome. The pair-wise sequence analysis showed 92–100 nt identity among the present CTV isolates. Phylogenetic tree analysis segregated the present isolates into two genogroups; of which 16 isolates clustered into one genogroup along with the decline CTV strain VT/Kpg3, and the remaining isolates into another genogroup along with Indian CTV isolate AR-1. Intra-farm genetic diversity among CTV isolates were observed in citrus orchards. The present study revealed that decline inducing CTV genotype VT/Kpg3 is prevalent in citrus growing areas of Assam of NE India.